scout-browser 4.92__py3-none-any.whl → 4.95.0__py3-none-any.whl

scout/server/blueprints/variant/templates/variant/tx_overview.html

@@ -76,15 +76,15 @@
               </td> <!-- end of ID col-->
 
               <td> <!-- HGVS Description col -->
-                {% set hgvs_c = (tx.coding_sequence_name or '')|truncate(20, True) %}
+                {% set hgvs_c = (tx.coding_sequence_name or '')|truncate(30, True) %}
                 {% if variant.chromosome in ["MT","M"] %}
                   {% set mt_notation = "m." ~ variant.position ~ variant.reference ~ ">" ~ variant.alternative %}
-                  {{ mt_notation|truncate(20,True) }} <span class="text-muted">({{ hgvs_c }})</span>
+                  {{ mt_notation|truncate(30,True) }} <span class="text-muted">({{ hgvs_c }})</span>
                 {% else %}
                   {{ hgvs_c }}
                 {% endif %}
                 <span class="text-muted float-end">
-                  {{ (tx.protein_sequence_name or '')|url_decode }}
+                  {{ (tx.protein_sequence_name or '')|url_decode|truncate(30, True) }}
                 </span>
               </td> <!-- end of HGVS Description col -->
 

scout/server/blueprints/variant/templates/variant/variant.html

@@ -84,7 +84,7 @@
 
     <div class="row">
       <div class="col-lg-3 col-md-6">
-        {{ panel_classify(variant, institute, case, ACMG_OPTIONS, manual_rank_options, cancer_tier_options, dismiss_variant_options, mosaic_variant_options, evaluations) }}
+        {{ panel_classify(variant, institute, case, ACMG_OPTIONS, CCV_OPTIONS, manual_rank_options, cancer_tier_options, dismiss_variant_options, mosaic_variant_options, evaluations, ccv_evaluations) }}
       </div>
       <div class="col-lg-5 col-md-6">
         {{ panel_summary() }}

scout/server/blueprints/variant/templates/variant/variant_details.html

@@ -200,6 +200,20 @@
   </div>
 {% endmacro %}
 
+{% macro observation_badge(observed_case) %}
+
+  {% if observed_case.variant and observed_case.variant.category == "snv"%}
+  <a class="badge rounded-pill bg-light text-dark" target="_blank" href="{{ url_for('variant.variant', institute_id=observed_case.case.owner, case_name=observed_case.case.display_name, variant_id=observed_case.variant._id) }}">{{ observed_case.case.display_name }}</a>
+  {% elif observed_case.variant and observed_case.variant.category == "sv"%}
+  <a class="badge rounded-pill bg-light text-dark" target="_blank" href="{{ url_for('variant.sv_variant', institute_id=observed_case.case.owner, case_name=observed_case.case.display_name, variant_id=observed_case.variant._id) }}">{{ observed_case.case.display_name }}</a>
+  {% else %}
+  <span data-bs-toggle="tooltip" title="Missing link, this might be caused by variants not loaded after a rerun or inexact SV matching.">
+    <span class="ml-3 badge rounded-pill bg-light text-dark">{{ observed_case.case.display_name }}</span>
+  </span>
+  {% endif %}
+
+{% endmacro %}
+
 {% macro observations_panel(variant, observations, case) %}
   <div class="card panel-default">
     <div class="panel-heading d-flex justify-content-between">
@@ -240,19 +254,23 @@
                      </span>
                   {% endif %}
                   {% endif %}
-                  {% for data in obs.cases %}
-                     {% if data.variant and data.variant.category == "snv"%}
-                       <a class="badge rounded-pill bg-light text-dark" target="_blank" href="{{ url_for('variant.variant', institute_id=data.case.owner, case_name=data.case.display_name, variant_id=data.variant._id) }}">{{ data.case.display_name }}</a>
-                     {% elif data.variant and data.variant.category == "sv"%}
-                       <a class="badge rounded-pill bg-light text-dark" target="_blank" href="{{ url_for('variant.sv_variant', institute_id=data.case.owner, case_name=data.case.display_name, variant_id=data.variant._id) }}">{{ data.case.display_name }}</a>
-                     {% else %}
-                       <span data-bs-toggle="tooltip" title="Missing link, this might be caused by variants not loaded after a rerun or inexact SV matching.">
-                         <span class="ml-3 badge rounded-pill bg-light text-dark">{{ data.case.display_name }}</span>
-                       </span>
-                     {% endif %}
+                  {% for observed_case in obs.cases %}
+                    {% if loop.index <= 10 %}
+                      {{ observation_badge(observed_case) }}
+                    {% endif %}
                   {% endfor %}
+
                   {% if obs.cases|length > 10 %}
-                     + more
+                    <span class="collapse" id="additionalCases_{{ loqusid }}">
+                      {% for observed_case in obs.cases %}
+                        {% if loop.index > 10 %}
+                          {{ observation_badge(observed_case) }}
+                        {% endif %}
+                      {% endfor %}
+                    </span>
+                    <button class="btn btn-link p-0 toggle-button" type="button" data-bs-toggle="collapse" href="#additionalCases_{{ loqusid }}">
+                      <span class="toggle-text">Show more/less</span>
+                    </button>
                   {% endif %}
                 </td>
               </tr>

scout/server/blueprints/variant/utils.py

@@ -2,7 +2,14 @@ import logging
 from typing import Dict, List, Optional, Tuple
 
 from scout.adapter import MongoAdapter
-from scout.constants import ACMG_COMPLETE_MAP, CALLERS, CLINSIG_MAP, SO_TERMS, VARIANT_FILTERS
+from scout.constants import (
+    ACMG_COMPLETE_MAP,
+    CALLERS,
+    CCV_COMPLETE_MAP,
+    CLINSIG_MAP,
+    SO_TERMS,
+    VARIANT_FILTERS,
+)
 from scout.server.links import add_gene_links, add_tx_links
 
 LOG = logging.getLogger(__name__)
@@ -472,6 +479,19 @@ def evaluation(store, evaluation_obj):
     return evaluation_obj
 
 
+def ccv_evaluation(store, evaluation_obj):
+    """Fetch and fill-in evaluation object."""
+    evaluation_obj["institute"] = store.institute(evaluation_obj["institute_id"])
+    evaluation_obj["case"] = store.case(evaluation_obj["case_id"])
+    evaluation_obj["variant"] = store.variant(evaluation_obj["variant_specific"])
+    evaluation_obj["ccv_criteria"] = {
+        criterion["term"]: criterion for criterion in evaluation_obj["ccv_criteria"]
+    }
+    evaluation_obj["ccv_classification"] = CCV_COMPLETE_MAP.get(
+        evaluation_obj["ccv_classification"]
+    )
+
+
 def transcript_str(transcript_obj, gene_name=None):
     """Generate amino acid change as a string.
 

scout/server/blueprints/variant/views.py

@@ -13,13 +13,26 @@ from flask import (
 from flask_login import current_user
 from markupsafe import Markup
 
-from scout.constants import ACMG_CRITERIA, ACMG_MAP, ACMG_OPTIONS
-from scout.server.blueprints.variant.controllers import check_reset_variant_classification
+from scout.constants import (
+    ACMG_CRITERIA,
+    ACMG_MAP,
+    ACMG_OPTIONS,
+    CCV_CRITERIA,
+    CCV_MAP,
+    CCV_OPTIONS,
+)
+from scout.server.blueprints.variant.controllers import ccv_evaluation as ccv_evaluation_controller
+from scout.server.blueprints.variant.controllers import (
+    check_reset_variant_ccv_classification,
+    check_reset_variant_classification,
+)
 from scout.server.blueprints.variant.controllers import evaluation as evaluation_controller
 from scout.server.blueprints.variant.controllers import observations, str_variant_reviewer
 from scout.server.blueprints.variant.controllers import variant as variant_controller
 from scout.server.blueprints.variant.controllers import variant_acmg as acmg_controller
 from scout.server.blueprints.variant.controllers import variant_acmg_post
+from scout.server.blueprints.variant.controllers import variant_ccv as ccv_controller
+from scout.server.blueprints.variant.controllers import variant_ccv_post
 from scout.server.blueprints.variant.verification_controllers import (
     MissingVerificationRecipientError,
     variant_verification,
@@ -27,6 +40,7 @@ from scout.server.blueprints.variant.verification_controllers import (
 from scout.server.extensions import loqusdb, store
 from scout.server.utils import institute_and_case, public_endpoint, templated
 from scout.utils.acmg import get_acmg, get_acmg_conflicts, get_acmg_temperature
+from scout.utils.ccv import get_ccv, get_ccv_conflicts, get_ccv_temperature
 from scout.utils.ensembl_rest_clients import EnsemblRestApiClient
 
 LOG = logging.getLogger(__name__)
@@ -205,9 +219,40 @@ def variant_acmg(institute_id, case_name, variant_id):
     )
 
 
+@variant_bp.route("/<institute_id>/<case_name>/<variant_id>/ccv", methods=["GET", "POST"])
+@templated("variant/ccv.html")
+def variant_ccv(institute_id, case_name, variant_id):
+    """ClinGen-CCG-VICC classification form."""
+    if request.method == "GET":
+        data = ccv_controller(store, institute_id, case_name, variant_id)
+        return data
+
+    criteria = []
+    criteria_terms = request.form.getlist("criteria")
+    for term in criteria_terms:
+        criteria.append(
+            dict(
+                term=term,
+                comment=request.form.get("comment-{}".format(term)),
+                links=[request.form.get("link-{}".format(term))],
+            )
+        )
+    ccv = variant_ccv_post(store, institute_id, case_name, variant_id, current_user.email, criteria)
+    flash("classified as: {}".format(ccv), "info")
+    return redirect(
+        url_for(
+            ".variant",
+            institute_id=institute_id,
+            case_name=case_name,
+            variant_id=variant_id,
+        )
+    )
+
+
 @variant_bp.route("/<institute_id>/<case_name>/<variant_id>/update", methods=["POST"])
 def variant_update(institute_id, case_name, variant_id):
-    """Update user-defined information about a variant: manual rank & ACMG."""
+    """Update user-defined information about a variant: manual rank, cancer tier,
+    CLinGen-CGC-VICC classification, dismissal & mosaic tags."""
     institute_obj, case_obj = institute_and_case(store, institute_id, case_name)
     variant_obj = store.variant(variant_id)
     user_obj = store.user(current_user.email)
@@ -250,6 +295,7 @@ def variant_update(institute_id, case_name, variant_id):
             flash("Variant tag was updated", "info")
         else:
             flash("Variant tag was reset", "info")
+
     elif request.form.get("acmg_classification"):
         new_acmg = request.form["acmg_classification"]
         acmg_classification = variant_obj.get("acmg_classification")
@@ -268,6 +314,24 @@ def variant_update(institute_id, case_name, variant_id):
         )
         flash("updated ACMG classification: {}".format(new_acmg), "info")
 
+    elif request.form.get("ccv_classification"):
+        new_ccv = request.form["ccv_classification"]
+        ccv_classification = variant_obj.get("ccv_classification")
+        # If there already is a classification and the same one is sent again this means that
+        # We want to remove the classification
+        if isinstance(ccv_classification, int) and (new_ccv == CCV_MAP[ccv_classification]):
+            new_ccv = None
+
+        store.submit_ccv_evaluation(
+            variant_obj=variant_obj,
+            user_obj=user_obj,
+            institute_obj=institute_obj,
+            case_obj=case_obj,
+            link=link,
+            classification=new_ccv,
+        )
+        flash("updated ClinGen-CGC-VIGG classification: {}".format(new_ccv), "info")
+
     new_dismiss = request.form.getlist("dismiss_variant")
     if new_dismiss:
         store.update_dismiss_variant(
@@ -310,7 +374,6 @@ def variant_update(institute_id, case_name, variant_id):
 @templated("variant/acmg.html")
 def evaluation(evaluation_id):
     """Show, edit or delete an ACMG evaluation."""
-
     evaluation_obj = store.get_evaluation(evaluation_id)
     if evaluation_obj is None:
         flash("Evaluation was not found in database", "warning")
@@ -328,7 +391,7 @@ def evaluation(evaluation_id):
         if check_reset_variant_classification(store, evaluation_obj, link):
             flash("Cleared ACMG classification.", "info")
 
-        return redirect(link)
+        return redirect(request.referrer)
 
     return dict(
         evaluation=evaluation_obj,
@@ -353,6 +416,53 @@ def acmg():
     return jsonify({"classification": classification, "conflicts": acmg_conflicts, **acmg_bayesian})
 
 
+@variant_bp.route("/ccv_evaluations/<evaluation_id>", methods=["GET", "POST"])
+@templated("variant/ccv.html")
+def ccv_evaluation(evaluation_id):
+    """Show, edit or delete an ClinGen-CGC-VIGG evaluation."""
+
+    evaluation_obj = store.get_ccv_evaluation(evaluation_id)
+    if evaluation_obj is None:
+        flash("Evaluation was not found in database", "warning")
+        return redirect(request.referrer)
+    ccv_evaluation_controller(store, evaluation_obj)
+    if request.method == "POST":
+        link = url_for(
+            ".variant",
+            institute_id=evaluation_obj["institute"]["_id"],
+            case_name=evaluation_obj["case"]["display_name"],
+            variant_id=evaluation_obj["variant_specific"],
+        )
+        store.delete_ccv_evaluation(evaluation_obj)
+
+        if check_reset_variant_ccv_classification(store, evaluation_obj, link):
+            flash("Cleared ClinGen-CGC-VIGG classification.", "info")
+
+        return redirect(link)
+
+    return dict(
+        evaluation=evaluation_obj,
+        edit=bool(request.args.get("edit")),
+        institute=evaluation_obj["institute"],
+        case=evaluation_obj["case"],
+        variant=evaluation_obj["variant"],
+        CRITERIA=CCV_CRITERIA,
+        CCV_OPTIONS=CCV_OPTIONS,
+    )
+
+
+@variant_bp.route("/api/v1/ccv")
+@public_endpoint
+def ccv():
+    """Calculate an ClinGen-CVC-VIGG classification from submitted criteria."""
+    criteria = request.args.getlist("criterion")
+    classification = get_ccv(criteria)
+
+    ccv_bayesian = get_ccv_temperature(criteria)
+    ccv_conflicts = get_ccv_conflicts(criteria)
+    return jsonify({"classification": classification, "conflicts": ccv_conflicts, **ccv_bayesian})
+
+
 @variant_bp.route(
     "/<institute_id>/<case_name>/<variant_id>/<order>",
     methods=["POST"],

scout/server/blueprints/variants/controllers.py

@@ -17,6 +17,8 @@ from scout.constants import (
     CANCER_EXPORT_HEADER,
     CANCER_SPECIFIC_VARIANT_DISMISS_OPTIONS,
     CANCER_TIER_OPTIONS,
+    CCV_COMPLETE_MAP,
+    CCV_MAP,
     CHROMOSOMES,
     CHROMOSOMES_38,
     CLINSIG_MAP,
@@ -362,6 +364,7 @@ def get_manual_assessments(variant_obj):
     ## display manual input of interest: classified, commented, tagged, mosaicism or dismissed.
     assessment_keywords = [
         "acmg_classification",
+        "ccv_classification",
         "manual_rank",
         "cancer_tier",
         "dismiss_variant",
@@ -402,6 +405,16 @@ def get_manual_assessments(variant_obj):
                 assessment["label"] = classification["short"]
                 assessment["display_class"] = classification["color"]
 
+            if assessment_type == "ccv_classification":
+                ccv_classification = variant_obj[assessment_type]
+                if isinstance(ccv_classification, int):
+                    ccv_code = CCV_MAP[ccv_classification]
+                    ccv_classification = CCV_COMPLETE_MAP[ccv_code]
+
+                assessment["title"] = "ClinGen-CGC-VIGG: {}".format(ccv_classification["label"])
+                assessment["label"] = ccv_classification["short"]
+                assessment["display_class"] = ccv_classification["color"]
+
             if assessment_type == "dismiss_variant":
                 dismiss_variant_options = {
                     **DISMISS_VARIANT_OPTIONS,
@@ -918,6 +931,11 @@ def parse_variant(
         acmg_code = ACMG_MAP[variant_obj["acmg_classification"]]
         variant_obj["acmg_classification"] = ACMG_COMPLETE_MAP[acmg_code]
 
+    ccv_classification = variant_obj.get("ccv_classification")
+    if isinstance(ccv_classification, int):
+        ccv_code = CCV_MAP[variant_obj["ccv_classification"]]
+        variant_obj["ccv_classification"] = CCV_COMPLETE_MAP[ccv_code]
+
     # convert length for SV variants
     variant_length = variant_obj.get("length")
     variant_obj["length"] = {100000000000: "inf", -1: "n.d."}.get(variant_length, variant_length)
@@ -1409,6 +1427,19 @@ def cancer_variants(store, institute_id, case_name, variants_query, variant_coun
                     secondary_gene = gene
         variant_obj["second_rep_gene"] = secondary_gene
         variant_obj["clinical_assessments"] = get_manual_assessments(variant_obj)
+
+        evaluations = []
+        # Get previous ClinGen-CGC-VIGG evaluations of the variant from other cases
+        for evaluation_obj in store.get_ccv_evaluations(variant_obj):
+            if evaluation_obj["case_id"] == case_obj["_id"]:
+                continue
+
+            ccv_classification = evaluation_obj["ccv_classification"]
+
+            evaluation_obj["ccv_classification"] = CCV_COMPLETE_MAP.get(ccv_classification)
+            evaluations.append(evaluation_obj)
+        variant_obj["ccv_evaluations"] = evaluations
+
         variants_list.append(variant_obj)
 
     data = dict(

scout/server/blueprints/variants/forms.py

@@ -16,7 +16,7 @@ from wtforms import (
     SubmitField,
     validators,
 )
-from wtforms.widgets import TextInput
+from wtforms.widgets import NumberInput, TextInput
 
 from scout.constants import (
     CALLERS,
@@ -132,8 +132,22 @@ class VariantFiltersForm(FlaskForm):
     )
 
     chrom = NonValidatingSelectMultipleField("Chromosome", choices=[], default="")
-    start = IntegerField("Start position", [validators.Optional()])
-    end = IntegerField("End position", [validators.Optional()])
+    start = IntegerField(
+        "Start position",
+        [
+            validators.Optional(),
+            validators.NumberRange(min=0, message="Start position must be 1 or greater."),
+        ],
+        widget=NumberInput(min=1),
+    )
+    end = IntegerField(
+        "End position",
+        [
+            validators.Optional(),
+            validators.NumberRange(min=0, message="End position must be 1 or greater."),
+        ],
+        widget=NumberInput(min=1),
+    )
     cytoband_start = NonValidatingSelectField("Cytoband start", choices=[])
     cytoband_end = NonValidatingSelectField("Cytoband end", choices=[])
 
@@ -264,8 +278,22 @@ class OutlierFiltersForm(FlaskForm):
     )
 
     chrom = NonValidatingSelectMultipleField("Chromosome", choices=[], default="")
-    start = IntegerField("Start position", [validators.Optional()])
-    end = IntegerField("End position", [validators.Optional()])
+    start = IntegerField(
+        "Start position",
+        [
+            validators.Optional(),
+            validators.NumberRange(min=1, message="Start position must be 0 or greater."),
+        ],
+        widget=NumberInput(min=1),
+    )
+    end = IntegerField(
+        "End position",
+        [
+            validators.Optional(),
+            validators.NumberRange(min=1, message="End position must be 0 or greater."),
+        ],
+        widget=NumberInput(min=1),
+    )
     cytoband_start = NonValidatingSelectField("Cytoband start", choices=[])
     cytoband_end = NonValidatingSelectField("Cytoband end", choices=[])
 

scout/server/blueprints/variants/templates/variants/cancer-sv-variants.html

@@ -1,6 +1,6 @@
 {% extends "layout.html" %}
 {% from "variants/utils.html" import cancer_sv_filters,cell_rank, pagination_footer, pagination_hidden_div, filter_form_footer, filter_script_main, update_stash_filter_button_status, dismiss_variants_block, callers_cell %}
-{% from "variants/components.html" import external_scripts, external_stylesheets, frequency_cell_general, observed_cell_general, variant_gene_symbols_cell, variant_funct_anno_cell %}
+{% from "variants/components.html" import allele_cell, external_scripts, external_stylesheets, frequency_cell_general, observed_cell_general, variant_gene_symbols_cell, variant_funct_anno_cell %}
 
 {% block title %}
   {{ super() }} - {{ institute.display_name }} - {{ case.display_name }} - SV variants
@@ -111,8 +111,8 @@
       {{ variant.sub_category|upper }}
     </td>
     <td>{{ variant.chromosome if variant.chromosome == variant.end_chrom else variant.chromosome+'-'+variant.end_chrom }}</td>
-    <td class="col-2"><span style="white-space: nowrap;">{{ variant.position|human_longint|safe }}</span></td>
-    <td class="col-2"><span style="white-space: nowrap;">{{ 'inf' if variant.end == 100000000000 else variant.end|human_longint|safe }}</span></td>
+    <td class="col-2">{% if variant.chromosome != variant.end_chrom %}<span class="text-body"></span><b>{{ variant.chromosome }}</b>:</span>{% endif %}<span class="text-body" style="white-space: nowrap;">{{ variant.position|human_longint|safe }}</span></td>
+    <td class="col-2">{% if variant.chromosome != variant.end_chrom %}<span class="text-body"><b>{{ variant.end_chrom }}</b>:</span>{% endif %}<span style="white-space: nowrap;">{{ 'inf' if variant.end == 100000000000 else variant.end|human_longint|safe }}</span></td>
     <td class="col-2"><span style="white-space: nowrap;">{{ '-' if variant.length == 100000000000 else variant.length|human_longint|safe }}</span></td>
     <td class="text-end">{{ frequency_cell_general(variant) }}</td>
     <td>{{observed_cell_general(variant)}}</td>
@@ -122,25 +122,11 @@
     <td>
       {{ variant_funct_anno_cell(variant) }}
     </td>
-    <td>{{ allele_cell(variant.tumor or {}) }}{% if variant.somatic_score %}<small class="text-muted">[{{ variant.somatic_score }}]</small>{% endif %}</td>
+    <td>{{ allele_cell(variant.tumor or {}) }}{% if variant.somatic_score %}<small class="text-body" data-bs-toggle="tooltip" data-bs-placement="top" title="SV caller (Manta) somatic score">[{{ variant.somatic_score }}]</small>{% endif %}</td>
     <td>{{ allele_cell(variant.normal or {}) }}</td>
   </tr>
 {% endmacro %}
 
-{% macro allele_cell(allele) %}
-  {% if 'alt_freq' in allele %}
-    {% if allele.alt_freq == -1 %}
-      <span class="text-muted">.</span>
-    {% else %}
-      {{ allele.alt_freq|round(4) }}
-    {% endif %}
-    <br>
-    <small class="text-muted">{% if allele.alt_depth >= 0 %}{{ allele.alt_depth }}{% else %}.{% endif %}|{% if allele.ref_depth >= 0 %}{{ allele.ref_depth }}{% else %}.{% endif %}</small>
-  {% else %}
-    <span class="text-muted">N/A</span>
-  {% endif %}
-{% endmacro %}
-
 
 {% block scripts %}
   {{ super() }}

scout/server/blueprints/variants/templates/variants/cancer-variants.html

@@ -1,8 +1,8 @@
 {% extends "layout.html" %}
 
-{% from "variants/components.html" import external_scripts, external_stylesheets, gene_cell, frequency_cell_general, observed_cell_general, variant_funct_anno_cell %}
+{% from "variants/components.html" import allele_cell, external_scripts, external_stylesheets, gene_cell, frequency_cell_general, observed_cell_general, variant_funct_anno_cell %}
 {% from "variants/utils.html" import cancer_filters, cell_rank, pagination_footer, pagination_hidden_div, dismiss_variants_block, filter_form_footer, filter_script_main, update_stash_filter_button_status, callers_cell %}
-{% from "variants/indicators.html" import pin_indicator, causative_badge, clinical_assessments_badge, comments_badge, dismissals_badge, evaluations_badge, group_assessments_badge, matching_manual_rank, other_tiered_variants, research_assessments_badge %}
+{% from "variants/indicators.html" import pin_indicator, causative_badge, clinical_assessments_badge, comments_badge, dismissals_badge, evaluations_badge, ccv_evaluations_badge, group_assessments_badge, matching_manual_rank, other_tiered_variants, research_assessments_badge %}
 
 {% block title %}
   {{ variant_type|capitalize }} somatic variants
@@ -109,6 +109,7 @@
               {{ comments_badge(case, institute, variant) }}
               {{ causative_badge(variant, case) }}
               {{ other_tiered_variants(variant) }}
+              {{ ccv_evaluations_badge(variant) }}
             </td>
             <td>{{ rank_cell(variant) }}</td>
             <td>{{ cadd_cell(variant) }}</td>
@@ -174,17 +175,7 @@
 {% endmacro %}
 
 {% macro position_cell(variant) %}
-  {{ variant.chromosome }}<span class="text-muted">:{{ variant.position }}</span>
-{% endmacro %}
-
-{% macro allele_cell(allele) %}
-  {% if 'alt_freq' in allele %}
-    {{ allele.alt_freq|round(4)  }}
-    <br>
-    <small class="text-muted">{{ allele.alt_depth }} | {{ allele.ref_depth }}</small>
-  {% else %}
-    <span class="text-muted">N/A</span>
-  {% endif %}
+  <span class="text-body"><b>{{ variant.chromosome }}</b>:{{ variant.position }}</span>
 {% endmacro %}
 
 {% block scripts %}